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 metagenomeSeq: Statistical analysis for sparse highthroughput sequencing
 ssPerm: class permutations for smoothingspline time series analysis
class permutations for smoothingspline time series analysis
Description
Creates a list of permuted class memberships for the time series permuation tests.
Usage
1 
Arguments
df 
Data frame containing class membership and sample/patient id label. 
B 
Number of permutations. 
Value
A list of permutted class memberships
See Also
cumNorm
fitTimeSeries
ssFit
ssPermAnalysis
ssIntervalCandidate
Examples
1  # Not run

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 aggregateBySample: Aggregates a MRexperiment object or counts matrix to by a...
 aggregateByTaxonomy: Aggregates a MRexperiment object or counts matrix to a...
 biom2MRexperiment: Biom to MRexperiment objects
 calcNormFactors: Cumulative sum scaling (css) normalization factors
 calcPosComponent: Positive component
 calcShrinkParameters: Calculate shrinkage parameters
 calcStandardError: Calculate the zeroinflated lognormal statistic's standard...
 calculateEffectiveSamples: Estimated effective samples per feature
 calcZeroAdjustment: Calculate the zeroinflated component's adjustment factor
 calcZeroComponent: Zero component
 correctIndices: Calculate the correct indices for the output of...
 correlationTest: Correlation of each row of a matrix or MRexperiment object
 cumNorm: Cumulative sum scaling normalization
 cumNormMat: Cumulative sum scaling factors.
 cumNormStat: Cumulative sum scaling percentile selection
 cumNormStatFast: Cumulative sum scaling percentile selection
 doCountMStep: Compute the Maximization step calculation for features still...
 doEStep: Compute the Expectation step.
 doZeroMStep: Compute the zero Maximization step.
 exportMat: Export the normalized MRexperiment dataset as a matrix.
 exportStats: Various statistics of the count data.
 expSummary: Access MRexperiment object experiment data
 extractMR: Extract the essentials of an MRexperiment.
 filterData: Filter datasets according to no. features present in features...
 fitDO: Wrapper to calculate Discovery Odds Ratios on feature values.
 fitFeatureModel: Computes differential abundance analysis using a...
 fitLogNormal: Computes a lognormal linear model and permutation based...
 fitMultipleTimeSeries: Discover differentially abundant time intervals for all...
 fitPA: Wrapper to run fisher's test on presence/absence of a...
 fitSSTimeSeries: Discover differentially abundant time intervals using...
 fitTimeSeries: Discover differentially abundant time intervals
 fitZeroLogNormal: Compute the log foldchange estimates for the zeroinflated...
 fitZig: Computes the weighted foldchange estimates and tstatistics.
 getCountDensity: Compute the value of the count density function from the...
 getEpsilon: Calculate the relative difference between iterations of the...
 getNegativeLogLikelihoods: Calculate the negative loglikelihoods for the various...
 getPi: Calculate the mixture proportions from the zero model / spike...
 getZ: Calculate the current Z estimate responsibilities (posterior...
 isItStillActive: Function to determine if a feature is still active.
 libSize: Access sample depth of coverage from MRexperiment object
 libSizeset: Replace the library sizes in a MRexperiment object
 loadBiom: Load objects organized in the Biom format.
 loadMeta: Load a count dataset associated with a study.
 loadMetaQ: Load a count dataset associated with a study set up in a...
 loadPhenoData: Load a clinical/phenotypic dataset associated with a study.
 lungData: OTU abundance matrix of samples from a smoker/nonsmoker...
 makeLabels: Function to make labels simpler
 mergeMRexperiments: Merge two MRexperiment objects together
 mergeTable: Merge two tables
 metagenomeSeqdeprecated: Depcrecated functions in the metagenomeSeq package.
 metagenomeSeqpackage: Statistical analysis for sparse highthroughput sequencing
 mouseData: OTU abundance matrix of mice samples from a diet longitudinal...
 MRcoefs: Table of topranked features from fitZig or fitFeatureModel
 MRcounts: Accessor for the counts slot of a MRexperiment object
 MRexperiment2biom: MRexperiment to biom objects
 MRexperimentclass: Class "MRexperiment"  a modified eSet object for the data...
 MRfulltable: Table of top microbial marker gene from linear model fit...
 MRtable: Table of top microbial marker gene from linear model fit...
 newMRexperiment: Create a MRexperiment object
 normFactors: Access the normalization factors in a MRexperiment object
 normFactorsset: Replace the normalization factors in a MRexperiment object
 plotBubble: Basic plot of binned vectors.
 plotClassTimeSeries: Plot abundances by class
 plotCorr: Basic correlation plot function for normalized or...
 plotFeature: Basic plot function of the raw or normalized data.
 plotGenus: Basic plot function of the raw or normalized data.
 plotMRheatmap: Basic heatmap plot function for normalized counts.
 plotOrd: Plot of either PCA or MDS coordinates for the distances of...
 plotOTU: Basic plot function of the raw or normalized data.
 plotRare: Plot of rarefaction effect
 plotTimeSeries: Plot difference function for particular bacteria
 posteriorProbs: Access the posterior probabilities that results from analysis
 returnAppropriateObj: Check if MRexperiment or matrix and return matrix
 ssFit: smoothingsplines anova fit
 ssIntervalCandidate: calculate interesting time intervals
 ssPerm: class permutations for smoothingspline time series analysis
 ssPermAnalysis: smoothingsplines anova fits for each permutation
 trapz: Trapezoidal Integration
 ts2MRexperiment: With a list of fitTimeSeries results, generate an...
 uniqueFeatures: Table of features unique to a group
 zigControl: Settings for the fitZig function